Modular Separation Mixed with main controller folder having sub folders

[eluser]xtremer360[/eluser]
Well the setup of the files is what I'm mainly focused on. Because I will be working with modules but I also need to take into account login and just the dashboard by itself and registration. Do I put those separately into the applications/controllers folder or make modules out of those or something. After looking around I haven't sen anyone post anything about their setups when its used.